Re: Error in code

Thank you Dr. Guyer.

I tried with other solvers and the LinearGMRESSolver seems to work  
better. I am not sure if I could use that, though I have a non- 
symmetric matrix (I have a convection term in my formulation). With  
this solver the memory error seems to be gone, but "invalid value  
encountered in log" error comes up and the program stops running.

I am still struggling to find where the bug is. Just for  
confirmation : Is this correct to combine a phase transformation term  
and a counter diffusion term to make one convection coefficient ?
I have got the following terms:

counterDiffusion = -2[(La - Lb)*p(phi) + Lb] * c.getFaceGrad()

phaseTransformation = [G + (1 - 2c)*(La - Lb)] * p(phi).getFaceGrad()  
+ (Wb - Wa) * g(phi).getFaceGrad()

convectionCoefficient = counterDiffusion + phaseTransformation

convectionCoefficient *= D*(1-c).getHarmonicFaceValue()/R*T

where, phi = phase field variable, c = composition
p(phi) and g(phi) are the interpolation function and double well  
function respectively.

D is the diffusivity. D = MRT/c(1-c) (as described in fipy examples)

G, La, Lb, Wa and Wb are all constants for the time being.

PS: I was wondering if you got a chance to look at my paper. Your  
review comments will be highly appreciated.

Thank you very much for your help.

Rashmi

On Jul 10, 2008, at July10,1:16 PM, Jonathan Guyer wrote:

>
>
> On Jul 10, 2008, at 9:58 AM, Rashmi Ranjan Mohanty wrote:
>
>> I am running a Fipy code with a system size of 400x400 mesh points  
>> on a Mac Pro 3GHz Dual-Intel Xeon processor with 2GB memory. After  
>> running few steps it stops with the following error message:
>>
>> python(1013) malloc: *** vm_allocate(size=7921664) failed (error  
>> code=3)
>> python(1013) malloc: *** error: can't allocate region
>> python(1013) malloc: *** set a breakpoint in szone_error to debug
>> malloc fails for local dworkptr[].Traceback (most recent call last):
>>  File "isothermal-new2D.py", line 355, in <module>
>>    compRes = compEq.sweep(var = comp, boundaryConditions = BCsC,  
>> dt=time, solver=solver)
>>  File "/sw/lib/python2.5/site-packages/fipy/terms/term.py", line  
>> 153, in sweep
>>    self._solveLinearSystem(var, solver, matrix, RHSvector)
>>  File "/sw/lib/python2.5/site-packages/fipy/terms/term.py", line  
>> 102, in _solveLinearSystem
>>    solver._solve(matrix, array, RHSvector)
>>  File "/sw/lib/python2.5/site-packages/fipy/solvers/ 
>> linearLUSolver.py", line 92, in _solve
>>    LU = superlu.factorize(L._getMatrix().to_csr())
>> MemoryError
>>
>> I guess it has something to do with memory, but could not figure  
>> out a solution.
>> I would appreciate your help.
>
>
> My suspicion would lie on your use of the LU solver. The PySparse  
> LU solver is robust, and often faster than the iterative solvers,  
> but it does so by using a great deal of memory.
>
> Have you tried other solvers?
>